Rchemcpp: An R package for computing the similarity of molecules

The functionality of
Chemcpp is provided in R, that is the computation of similarities between molecules by kernel functions.
The following kernels are implemented:

the marginalized graph kernel between labeled graphs

extensions of the marginalized kernel

Tanimoto kernels

graph kernels based on tree patterns

kernels based on pharmacophores for 3D structure of molecules

Input are molecules provided in the SDF format (MOL format) and output is a numeric kernel matrix. This kernel matrix easily be used in R for clustering and prediction tasks, like the prediction of toxicity or biological activity of a given molecule.